There is a researcher here who is getting this error in version 4.2.0, I have uploaded the 001.mgz to the ftp:

****************TEMPLATE DEFORMATION****************

      second estimation of the COG coord: x=150,y=117, z=145, r=8362 iterations

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1073730580

  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=20 , nb = -1073752625

  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1073753196

 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=5, CSF_MAX=26 , nb = -1601994905

 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = -1073752746

    OTHER      CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1768967209

mri_watershed Error:

 GLOBAL region of the brain empty !

Darwin lim44-macpro.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386